User: Marcus

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Marcus150
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Posts by Marcus

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problem with impute.knn in the impute package
... Hello. You have to remove the random seed using: if(exists(".Random.seed")) rm(.Random.seed) before you run the impute.knn function if you are using a Windows machine. Regards Marcus Marcus Gry Bj?rklund Royal Institute of Technology AlbaNova University Center Department of Molecular Bio ...
clustering impute written 13.5 years ago by Marcus150 • updated 13.5 years ago by He, Yiwen NIH/CIT360
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Answer: A: LIMMA : design (1, 2, 3, 3 ) , I gotEXCITINGresults, what could be the logic, si
... Hello all users. I have a question regarding the mean calculations of the M-values in LIMMA. I guess that the fit$coeff is the mean of the M-values used for the linear model. The fit$coeff has the mean value of the data derived from a specific RNA source (as defined in the design matrix), and the ...
written 13.5 years ago by Marcus150
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Answer: A: hgu133_plus_2?
... I guess that you can try something like: >memory.limit(size=1500) or whatever size you like. If you have a slow computer and a lot of data, you might have to wait for a long long time.. :) Marcus Gry Bj?rklund Royal Institute of Technology AlbaNova University Center Department of Molecular ...
written 13.7 years ago by Marcus150
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Answer: A: mas5call select genes
... Hello Bioc. I have encountered a problem when I try to use the impute.knn function in the package impute. I have tried to use a matrix with 30000 rows and 2 columns(MS). When I try the command: impute.knn(MS) Then R will crash within a second or so. Does anyone use the imputations in the packa ...
written 13.8 years ago by Marcus150
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FW: venn diagram in R
... Hmm..I forgot. In our function we use the vennDiagram function which is a part of the limma package. So U must have that package loaded. /M Hi. At our department we have made a small vennDiagram script. I am not sure if it suites your needs, but if you have vectors with text strings, for exampl ...
written 14.5 years ago by Marcus150
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Comment: C: venn diagram in R
... Hi. At our department we have made a small vennDiagram script. I am not sure if it suites your needs, but if you have vectors with text strings, for example: A <- c("test", "example", "common") B <- c("anything", "else", "common") C <- c("unique", "R", "Bioconductor") unique(A)->A un ...
written 14.5 years ago by Marcus150
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Fwd: Re: Fwd: Re: Clustering in R....
... >X-Mailer: QUALCOMM Windows Eudora Version 5.2.0.9 >Date: Thu, 27 Nov 2003 08:12:22 +0100 >To: Marcus >From: Johan Lindberg >Subject: Re: Fwd: Re: [BioC] Clustering in R.... >X-MIME-Autoconverted: from quoted-printable to 8bit by kiev.biotech.kth.se >id hAR7HNPr006352 > &g ...
visualization clustering convert written 14.9 years ago by Marcus150
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Limma issues.
... Hi limma users. I have some general questions regarding the use of dupcor.series and gls.series functions. I use an experimental design that compares three different conditions to a fourth (which I will call a reference). So the design of the experiment looks something like: Cond 1 ...
pathways limma written 14.9 years ago by Marcus150 • updated 14.9 years ago by Gordon Smyth35k
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Clustering in R....
... >Hello again. Back from some weeks of laborative work I still have some >questions on clustering in R. > >I got a lot of help from Sean Davis (thanks a lot :o) ) so if he or >someone else have the time.... > >My problem is that I have some spots flagges as NA in a matrix of M ...
clustering written 15.0 years ago by Marcus150 • updated 14.9 years ago by Sean Davis21k
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Fwd: Re: Fwd: Re: Heatmap function
... >Hello again... I still have some questions. If you have the time Sean (or >someone else) I would be very grateful. > >Yes, the M-values are log, but I have checked and I do not have any >infinite or NaN values in the matrix. > >I have som questions regarding hclust. It says th ...
clustering written 15.0 years ago by Marcus150

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Popular Question 13.5 years ago, created a question with more than 1,000 views. For Clustering in R....

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